8-78656057-G-T

Variant names:

• chr8-78656057-G-T
• rs4739135
• ENST00000661869.1:n.978+8948C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661869.1(ENSG00000286675):​n.978+8948C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,038 control chromosomes in the GnomAD database, including 44,916 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (44916 hom., cov: 31)
• Consequence: ENSG00000286675 ENST00000661869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

Genes affected

ENSG00000286675 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375911	XR_007060972.1	n.975+8948C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286675	ENST00000661869.1	n.978+8948C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116020 AN: 151920 Hom.: 44897 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.735

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.764 AC: 116085 AN: 152038 Hom.: 44916 Cov.: 31 AF XY: 0.765 AC XY: 56867 AN XY: 74320

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.735

Alfa AF: 0.774 Hom.: 4635

Bravo AF: 0.757

Asia WGS AF: 0.808 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4739135; hg19: chr8-79568292;